Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan

Shigella spp. are the most common cause of dysentery in developing countries and the second leading cause of diarrheal deaths worldwide. Multidrug-resistant (MDR) Shigella spp. are a serious threat to global health. Herein, we report draft genome sequences for three MDR Shigella isolates from Pakistan, two Shigella flexneri isolates and one Shigella sonnei isolate.

ABSTRACT

Shigella spp. are the most common cause of dysentery in developing countries and the second leading cause of diarrheal deaths worldwide. Multidrug-resistant (MDR) Shigella spp. are a serious threat to global health. Herein, we report draft genome sequences for three MDR Shigella isolates from Pakistan, two Shigella flexneri isolates and one Shigella sonnei isolate.

ANNOUNCEMENT

Among the Enterobacteriaceae, the genus Shigella is composed of four species (Shigella dysenteriae, Shigella flexneri, Shigella boydii, and Shigella sonnei) that cause severe diarrhea (1). Shigellosis is the most common cause of dysentery in developing countries and the second leading cause of diarrheal deaths worldwide (1). Rarely, Shigella spp. can also cause bacteremia, usually in children and immunocompromised adults (2, 3). The emergence of antimicrobial resistance (AMR) among Shigella spp. increasingly threatens the clinical management of shigellosis (4, 5). Multidrug-resistant (MDR) Shigella spp. are a serious threat to global health (6).

We report the draft genome sequences of three MDR Shigella isolates from Pakistan. The S. flexneri isolates were acquired from blood in 2015 (CFSAN059650) or stool (CFSAN059651 [original collection date unavailable]). The S. sonnei isolate (CFSAN059652) was obtained from stool in 2016. The isolates were obtained using standard culture methods, including growth on MacConkey agar, and identification and antimicrobial susceptibility testing were performed with the API 20E system and disk diffusion method (both bioMérieux), respectively (7). The results were confirmed with the Vitek 2 system (bioMérieux) and conventional broth microdilution (8). All isolates were resistant to ampicillin, cefazolin, ceftriaxone, cefotaxime, trimethoprim-sulfamethoxazole, and tetracycline. CFSAN059651 was resistant to cefepime, aztreonam, ampicillin-sulbactam, and chloramphenicol. CFSAN059650 and CFSAN059652 exhibited intermediate resistance against ciprofloxacin and ampicillin-sulbactam or against aztreonam and ceftazidime, respectively. Isolates were grown overnight in lysogeny broth (Lennox) at 37°C prior to DNA extraction using the DNeasy blood and tissue kit (Qiagen). DNA libraries were prepared via the Nextera XT DNA library kit (Illumina). Sequencing was performed on an Illumina MiSeq platform using the MiSeq reagent kit v2 (2 × 250-bp paired-end reads). Minimum average coverage (>50×) and read 1 (R1)/read 2 (R2) Q scores (>26) were set to ensure sequence quality. Sequence integrity (i.e., absence of contamination) was evaluated with Kraken (9, 10). Unless otherwise noted, default parameters were used in all analyses. De novo genome assemblies were created with Shovill 0.9 (https://github.com/tseemann/shovill), available in GalaxyTrakr (https://www.galaxytrakr.org) (11). The “trim reads” option was selected, and the minimum contig length was set at 500 bp. The draft genomes were submitted for annotation to the NCBI Prokaryotic Genome Annotation Pipeline (12). The number of reads, number of contigs, genome size, and GC content for each isolate are listed in Table 1.

TABLE 1.

Assembly statistics and accession numbers for the reported Shigella flexneri and Shigella sonnei genome sequences^a

Species and CFSAN IDb	NCBI BioSample accession no.	Yr of isolation	No. of contigs	Total length (bp)	N50 (bp)	GC content (%)	Genome coverage (×)	Coverage read count	Avg read quality (Q score [R1, R2])	SRR accession no.	WGS accession no.c
Shigella flexneri
CFSAN059650	SAMN10086692	2015	356	4,629,951	33,749	50.55	52	1,021,504	32, 26.6	SRR8836963	SSML00000000
CFSAN059651	SAMN10086664	NAd	359	4,620,515	31,916	50.45	69	1,373,334	32, 27	SRR8836950	SSMK00000000
Shigella sonnei
CFSAN059652	SAMN10086663	2016	384	4,528,736	25,093	50.85	71	1,388,868	32, 26.9	SRR8837012	SSMJ00000000

^aAll three clinical isolates belong to NCBI BioProject number PRJNA342326.

^bID, identifier.

^cWGS, whole-genome sequencing.

^dNA, not available.

ResFinder (13) was used to determine isolate sequence types (STs) based on in silico multilocus sequence typing (MLST) (14) and to identify AMR genes showing >99% identity to the reference gene sequences. The two S. flexneri isolates belonged to ST245, and the S. sonnei isolate belonged to ST152. CFSAN059650, CFSAN059651, and CFSAN059652 were found to harbor 10, 8, and 7 known AMR genes, respectively. All Shigella isolates carried drfA1, sul2, a CTX-M gene, and a tet gene. All isolates possessed AMR genes conferring resistance to β-lactams, aminoglycosides, trimethoprim, sulfonamides, and tetracyclines. Additional genes involved in resistance to fluoroquinolones (CFSAN059650 and CFSAN059652) or phenicol (CFSAN059651) were also observed. The data provided here offer a comparative genetic context for AMR in Shigella spp. that will inform infectious diseases epidemiology and be useful in public health monitoring.

Data availability.

The genome assemblies described herein are available in DDBJ/EMBL/GenBank under accession numbers SSMJ00000000, SSMK00000000, and SSML00000000. The versions here are the first versions. Other accession number data are presented in Table 1.